How to exclude third codon position from an analysis

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Fernando Carbayo

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May 18, 2020, 3:12:09 PM5/18/20
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Hi,

I am trying to run an analysis of a multiple aligment in IQ-Tree, including a COI fragment gene, the third position of its codons is saturated (charset Subset3). How can I exclude this third position? These are the parementers indicated by PartitionFinder2:

#nexus
begin sets;
    charset Subset1 = 1-1234;
    charset Subset2 = 1913-2524\3 1914-2524\3 1235-1912\3 1236-1912\3;
    charset Subset3 = 1237-1912\3;
    charset Subset4 = 1915-2524\3;

    charpartition PartitionFinder = TVM+I+G:Subset1, GTR+I+G:Subset2, TIM+I+G:Subset3, GTR+I+G:Subset4;
end;

Many thanks and stay healthy!

Fernando Carbayo

Minh Bui

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May 19, 2020, 3:39:05 AM5/19/20
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Hi Fernando,

Simply remove this charset line from the file, and also remove "TIM+I+G:Subset3” from the charpartition.

Minh 

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Fernando Carbayo

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May 19, 2020, 7:02:42 AM5/19/20
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Hi Minh,
Many tahnks for your quick and direct reply!

Best wishes,
Fernando Carbayo
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